Name: RenLab-HiC-cortex Rep2

Organism: Mus musculus

Source: Mouse cortex

RE: HindIII

Sample ID: GSM938751

Mapping Statistics

File SRR501778 SRR501779 SRR501780 SRR501781
Total reads 71,618,558 75,690,699 73,922,632 73,531,610
First pair aligned 64,063,239 (89.45%) 67,071,703 (88.61%) 65,828,103 (89.05%) 65,804,756 (89.49%)
Second pair aligned 62,699,476 (87.55%) 66,402,127 (87.73%) 65,014,114 (87.95%) 65,096,461 (88.53%)
PCR duplicate paired reads 2,751,941 (3.84%) 3,008,362 (3.97%) 2,928,604 (3.96%) 2,953,832 (4.02%)
Chimeric paired reads 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
Valid chimeric paired reads 0 (0.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
Total mapped/paired reads 41,728,375 (58.26%) 43,982,753 (58.11%) 43,171,696 (58.40%) 43,152,393 (58.69%)
Valid mapped/paired reads 38,976,434 (54.42%) 40,974,391 (54.13%) 40,243,092 (54.44%) 40,198,561 (54.67%)

HiC Read Statistics

Total reads 160,392,478
Chromosome not in fends 0 (0.00%)
PCR duplicates 0 (0.00%)
Outide RE cutsite range 1,470,056 (0.92%)
Insert larger than cutoff 53,690,259 (33.47%)
Fragment circularization 2,011,195 (1.25%)
Possible failed RE digest 12,803,093 (7.98%)
Valid cis reads 32,188,669 (20.07%)
Valid trans reads 58,229,206 (36.30%)
Unique cis fend pairs 26,083,749
Unique trans fend pairs 49,336,363

Insert Size Distribution

Fend Intra-chromosomal Interaction Distribution

Fend Inter-chromosomal Interaction Distribution

Best insert size

649